ost.seq.alg.renumber Namespace Reference

Functions
def	Renumber

Function Documentation

def ost.seq.alg.renumber.Renumber	(		seq_handle,
			sequence_number_with_attached_view = 1,
			old_number_label = None
	)

Function to renumber an entity according to an alignment between the model
sequence and the full-length target sequence. The aligned model sequence or
the alignment itself with an attached view needs to be provided. Upon
succcess, the renumbered entity is returned.
If an alignment is given, the first sequence of the alignment is considered
the full-length sequence and it must match the model sequence wherever it is
aligned (i.e. excluding gaps).

.. code-block:: python

  from ost.seq.alg import renumber
  from ost.bindings.clustalw import *
  ent = io.LoadPDB("path_to_model")
  s = io.LoadSequence("path_to_full_length_fasta_seqeunce")
  pdb_seq = seq.SequenceFromChain("model", ent.chains[0])
  aln = ClustalW(s, pdb_seq)
  aln.AttachView(1, ent.chains[0].Select(""))
  e = Renumber(aln.sequences[1])
  io.SavePDB(e, "renum.pdb")
 
:param seq_handle: Sequence or alignment handle with attached view.
:type seq_handle:  :class:`SequenceHandle` / :class:`AlignmentHandle`
:param sequence_number_with_attached_view: Sequence number for the aln. handle
                                           (not used if seq. handle given)
:type sequence_number_with_attached_view:  :class:`int`
:raises: :exc:`RuntimeError` if unknown type of *seq_handle* or if attached
         view is missing or if the given alignment sequence is inconsistent.

Definition at line 45 of file renumber.py.